Death is Only the Beginning
by Wind-Sorceress-Pluto
Summary: Mulder finds a letter addressed to him from Scully on his desk one morning and everything goes down hill from there... who killed her... will Mulder succeed in finding Scully's killer, and Scully for that matter! Find Out!
1. Prologue

Death is Only the Beginning

Don't own anything

...Prologue...

I am yours, I always have been, but I just need some time alone, some time to myself, some time to think. I think every night, as we lie down together, that I wish I was still just your partner in our basement office, away from all of the others, instead of your lover, at least then, you would have stopped whispering something you don't mean into my ear long enough to hear what I had to say. Any way, I've written to tell you this, that by the time you find me, I will be long gone, probably somewhere you will never find me. Have a happy life without my back to rub, or my shoulder to cry on, Mulder, and good luck with saving the X-Files next time Kersh decides to shut them down...

_Scully_

Mulder read the letter a second time to make sure his mind wasn't playing tricks on him, she was really gone, and he didn't understand why. He hadn't done anything wrong, had he? _If I did, she would have told me, wouldn't she have?_

He picked up the phone just as it rang and heard Skinner's voice on the other end, he quickly hung up the phone and headed for the parking garage and got into his car, driving off as fast as he was allowed to, hoping what he had just heard was not true. But he knew that if they had found Scully dead, and Skinner saw the body, then she was mist likely gone this time.

He reached her apartment in time to see Skinner trying to comfort a crying Maggie Scully, he gestured with his head to go into Scully's apartment. He slowly stepped into the room where the agents and investigators were standing, and sure enough, there she was, a bullet through the heart, and he couldn't believe it. There were no fingerprints on the gun, not enough of hers to now she had shot the gun. He knelt down next to his dead partner and looked to a pony-tailed cop bent down on her other side and he looked at Mulder.

"I am very sorry for your loss, Agent Mulder, but we have to take her to the morgue now, if you don't mind moving." He said quietly and apparently, Maggie Scully was close enough to hear this because a new set of tears was heard. Mrs. Scully had just gone through her daughter almost dying as it was, plus the loss of Melissa Scully three years ago. _Where did I go wrong, Scully? Was it my bad jokes, my attraction to Diana? Damn it Scully, you didn't have to go and get yourself killed you know?!_ He screamed in his mind as they lifted his partner into a body bag, zipped it up and carried it out. The pony-tailed cop looked at him again and wrote down a number on a piece of paper.

"If you have any kind of answers, anything at all that may help us, just give me a call, my name is Duncan MacLeod..."

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Okay peoples, this is not my first fanfic, of course it isn't, I don't want to sound too cocky, but I think it's okay, the idea just occurred to me, and here it is, anyway, if you like it, review PLEASE, I like those who review my other ones, but more would be nice! Thanx!


	2. Chapter One

Death is Only the Beginning

Don't own anything

...Chapter One...

I wonder if I should tell him, he has been apart of my life for nearly nine years, he deserves to know. But I can't tell him, he might take it the wrong way and expose it to the world, I don't want to become an outcast, I am tired of being an outcast to society. Anyway, maybe I should call him, ask him if I should tell Mulder... Would Xavier understand why I wanted so bad to tell Mulder? No, he's probably reading my thoughts right now, I have left my mind open for the past few months, it... it's just frustrating when you have to keep a secret from the man you trust with your life, and he keeps no secrets from you, and you have so many secrets kept from him... Maybe I should call Xavier... no, I'll deal with this on my own, no telling how much time I have left...

Mulder closed the book, it was the last entry before Scully was... he didn't want to think about it. He looked around Scully's empty apartment, he was looking for clues to who had murdered her, and when. He dug into his pocket for the piece of paper given to him by that detective, what was his name... MacLeod, that was it Duncan MacLeod. He found it and suddenly decided against it.

Why was he searching for help to an obvious X-Files? He was the one who had started the X-Files, and he did have two others to work with him, Agents Reyes and Doggett. He stuffed the number back into his pocket and went for the door, then he though for a moment... he got out his cell phone...he called her cell phone service provider and asked them for a list of her recent calls.

He walked into his office to see Reyes and Doggett looking at a list of numbers that had just come through the fax machine. They looked up only briefly, there were several numbers highlighted on the list.

"What did you find?" Mulder asked hoping that they had finally gotten a solid lead.

"Well, before we got this, the morgue called up to us, Scully's body has gone missing..." Reyes said and Doggett handed Mulder the list. "And there seems to be a number frequently called by her cell phone, a Duncan MacLeod, as we have confirmed..." Mulder's eyes widened and he reached for the paper in his pocket.

"What's the matter Agent Mulder? Do you know this guy?"

"Yeah, he's the detective on this case, met him when they called me to her apartment..." He said and reached for his cell phone, he dialed the number and waited for the man to answer it.

"MacLeod..." Came the monotone answer, Mulder heard someone moving in the backround.

"Yeah, this is Agent Mulder, we spoke briefly at my partner's apartment..." He paused and thought of how to approach this. "How did you know Scully?"

"We met a couple of years ago, and we kept in touch, why are you asking?" Mulder looked at the other two and then back at the paper in his hand.

"No reason at all..." Mulder lied and hung up, he set the paper on the desk and highlighted another number. "I want the name of the person who has this number as soon as possible." Mulder demanded and headed for the office door, grabbing the doorknob.

"What are you going to do?"

"Get some help..." And he left.

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Alright, finally some sort of answers! Can anyone guess which shows are crossed over with X-Files? Have I given enough clues? Anyway, read and review PLEASE!!!! 


	3. Chapter Two

Death is Only the Beginning

Don't own anything

…Chapter Two…

Mulder looked at the mansion in front of him, he slowly approached the door and was suddenly greeted by a woman with all white hair and she smiled warmly. She then led Mulder in, with no questions and to an office where a man in a wheelchair was sitting. The bald man then began talking,

"Agent Mulder, we've been expecting you…" He said and paused at Mulder's awkward reaction and then went on. "I am Professor Charles Xavier, this is my school for gifted youngsters, or as the public likes to call them, mutants. I am a telepath, I sensed you coming for a while now, and I made sure that we were ready for an questions you may ask about your partner's sudden death."

"How do you know about that?!" Mulder exclaimed, coming out of his passive mood and went on the offensive. The only one's who knew about it, were the police and the FBI, nothing about it had been released to the public. Suddenly he felt very funny, a tingling sensation and saw Xavier's eyes narrow.

"I am telepathic Mr. Mulder, I thought you understood that, or did Dana not tell you about herself to the extent of her ability?" Mulder looked shocked not for the first time since her death.

"She never even told me about you, or this Mac person she mentions a lot in her journal which I found recently…I came across you in the recent calls she made, and she called here, one or twice." He said. "And, do you know anything about the whereabouts of my partner's body, it disappeared from the morgue two days ago." Mulder sat down in front of Xavier's desk and the white haired woman left. Suddenly, the door swung open, much against the white haired woman's wishes.

"You cannot go in there Logan!" Mulder heard and he was suddenly yanked out of his seat and into the air. He came face to face with a weird hairstyle and brown eyes.

"What did you do to her you FBI bastard?!" He yelled into Mulder's face andMulder flinched.

"It's not a matter of what I did, it's a matter of what I am trying to do…" Mulder said and his assaulter, identified as Logan slowly let him down.

"That's not what I'm talking about, she called me, last week, crying goddammit!!!" Logan yelled, ready to slam Mulder into the wall again, he held in his anger and the urge to throw him out of the window. "Now, explain to me, why I shouldn't kill you where you stand?"

"Because I'm an FBI agent, you would get thrown in jail…"

"Tick tock, tick tock…"

"And would never do anything to hurt Scully!" Mulder said and then looked to Xavier. "At least, nothing that I recall anyway." Mulder looked away from the bald man, to the animal in front of him. "I don't even know who she is anymore, believing that she actually believed this."

"On the contrary Mr. Mulder, the only reason she tried to prove you wrong, is because the closer you got to the truth, the further you got from her, because the closer you got to the truth…"

"The closer to her secret you got, she didn't want you to hate her because of what she was, and when she called me, she said that you had left her." He said and then looked to the white-haired woman brushing past her and out of the office.

"Excuse him, he has a very bad temper, Agent Mulder, and this has been hard for all of us." Xavier rolled out from behind his desk and up to Mulder. "Scully came here as a child, her parents wanted help for her, she didn't have control over her mutant powers…"

"Wait, what mutant powers?" Mulder said, stopping the professor from rolling any further.

"Dana, well, she had the power to heal…"

"What's so dangerous about that?!" Mulder exclaimed, he didn't understand why he would keep something like this from him.

"Mr. Mulder, she had the power to heal, but that power also fed to her other power," He paused. "She could reverse the healing process with a thought, by an emotion, such as anger." Xavier looked up at the tall man, the man who had caused his student so much pain. "Mr. Mulder, you must understand, she was very secretive about this, she didn't like being different, she didn't want anything to happen to you because of her power."

"But, what did I do? Why did she…?"

"That is a question that you'd have to ask her, Mr. Mulder, even I couldn't get that deep into her mind to find that answer." Xavier looked at the door they were about to walk through when a girl came busting in, she had reddish-brown hair with white bangs, she closed the door behind her and looked to the professor.

"Professor, Logan's tearin' up the Danger Room."

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tell me what you guys think, i really want to know, even if you think bad of it 


	4. Chapter Three

Death is only the Beginning

Don't own anything but the plot

…Chapter Three…

I looked at the sky nowadays, and wonder if Mulder will say what he feels first, I can feel that he's just dying to tell me, but, I don't want to sound selfish, if he ever found out, what kind of power I had, then Cancerman would, and I'd be in a real shithole. Logan called last night, he's always checkin' up on me, I sometimes think that he is trying to win my heart, but he knows that I can only think of him as a brother, a best friend. When I first went to the mutant school run by Professor Xavier, I thought that my life would be a living hell, but they were the best years of my life. Now, I wish I was still there, learning to control my mutant powers, staying with Logan, 'Ro, and trying to get Rogue to talk more. Although she now has a boy running after her heart, some swamprat called Remy LeBeau, or Gambit, as he likes to be called. I can't help but think that those two are perfect for each other, of course, she can never touch him, thanks to her mutant power. Anyway, I'd better be going, Mulder's gonna wonder where I am if I don't show up for work soon.

Scully

Mulder looked up from the earlier entry in her journal, Reyes was seated in a chair next to Doggett, they sat in the cemetery where Melissa was buried, they were at her funeral, Scully's. The preacher's words fell on deaf ears, Maggie Scully was to busy crying her heart out, she had lost her two daughters and her husband, Reyes and Doggett were looking at him, but, Mulder knew they weren't listening, it was the same old thing. Mulder was too busy trying to figure out where he had gone wrong, why Scully had to go and commit suicide, or have someone kill her. He just didn't get. He felt a hand on his shoulder and looked up, he saw Rogue standing there, the girl from the Institute, she sat down next to him and he just broke down. As Scully used to do, Rogue cradled the grown man while he flushed the water from his system in an attempt to feel better. Then, Scully's coffin was lowered into the ground and dirt was thrown on top of it.

After the funeral, Mulder stayed with Mrs. Scully,

"Fox, you should really go home and get some rest, you have had a rough few days…" Maggie said as she unlocked the door to her house and she turned around to face Mulder. "Please, I'm okay, I promise I'll be okay, just go home and rest Fox." He nodded and walked back to his car and drove away.

He entered his apartment and went straight to his couch and fell on it, and tried to go to sleep, when he felt someone else in the room. He reached for his gun when he felt it wasn't there.

"So reckless, Mulder." He froze, he knew that voice, he looked around into the shadows and tried to find him.

"Krycek, what the hell do you want?!" Mulder yelled into the darkness and waited for an answer, when he didn't get one, he reached for the gun in his leg holster. He stopped when he felt a gun press against his forehead. He stopped and stood up and he put his hands up where the man could see them.

"I have something to tell you Mulder, but you must keep it a secret." Krycek whispered and waited for some kind of answer.

"What makes you think I want information from you Krycek?!" Mulder shot as Krycek pulled the gun away from Mulder's head.

"You have to know, that Scully isn't dead." Mulder turned around to find that Krycek wasn't there, and he was on the couch. He looked at his watch, it was 2 AM, he'd been sleeping, but was that really a dream?

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Tell me what ya think…!!! Was Mulder just dreaming, or was Krycek really there, but wait, wasn't Krycek dead???? Find out in the next chapter of Death is only the Beginning!!! 


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